Introduction “igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++.”
This procedure will identify sub-networks from a given network, using three clustering algorithms implemented by igraph: fast greedy, walktrap, and edge betweenness. The sub-networks will be further analyzed by enrichment analysis for their functional annotation.
The full network includes 467 nodes and 1496 edges (3.2 edges per nodes). For enrichment analysis, 466 nodes in the network can be mapped to one or more node sets, while there are totally 28850 unique nodes in all node sets. The background of the enrichment analysis has 21426 nodes. The maximum number of edges a node has is 53 and 118 (25.27%) nodes have only one edge.
Figure 1. Number of edges per nodes.
Figure 2A. Clustering via the fast greedy modularity optimization algorithm.
Figure 2B. Individual clusters identified via the fast greedy modularity optimization algorithm.
Table 1. Enrichment analysis of network clusters identified by the fast greedy algorithm.
| Cluster | Size | Core_Member | Top_Set | Top_OddsRatio | Top_PValue | Top_FDR |
|---|---|---|---|---|---|---|
| Cluster_1 | 93 | TP53 | h_all_33 | 21.50 | 0 | 1e-07 |
| Cluster_2 | 44 | RPS5; RPL19; RPS23; RPL15; RPL4; RPS7; RPL12; RPL10A | 491332 | 216.23 | 0 | 0e+00 |
| Cluster_3 | 40 | HSP90AA1 | 1127556 | 647.85 | 0 | 0e+00 |
| Cluster_4 | 119 | FYN | hsa05205 | 20.24 | 0 | 0e+00 |
| Cluster_5 | 28 | POLR1B; RPLP0 | 486555 | 123.41 | 0 | 0e+00 |
| Cluster_6 | 68 | POLR2A | 486891 | 34.91 | 0 | 0e+00 |
Figure 3A. Clustering via the Walktrap community finding algorithm.
Figure 3B. Individual clusters identified via the Walktrap community finding algorithm.
Table 2. Enrichment analysis of network clusters identified by the walkgrap algorithm.
| Cluster | Size | Core_Member | Top_Set | Top_OddsRatio | Top_PValue | Top_FDR |
|---|---|---|---|---|---|---|
| Cluster_1 | 76 | FYN | hsa04810 | 28.34 | 0 | 0.00e+00 |
| Cluster_2 | 46 | TP53; HSP90AA1 | c2_cp_BIOCARTA_88 | 153.25 | 0 | 1.55e-05 |
| Cluster_3 | 24 | NOP2 | 486555 | 122.00 | 0 | 0.00e+00 |
| Cluster_4 | 50 | POLR2A | 160950 | 73.82 | 0 | 0.00e+00 |
| Cluster_5 | 42 | RPS5; RPL19; POLR1B; RPS23; RPL15; RPL4; RPLP0; RPS7; RPL12; RPL10A | 491332 | 202.29 | 0 | 0.00e+00 |
Figure 4A. Clustering via the edge betweenness algorithm.
Figure 4B. Individual clusters identified via the edge betweenness algorithm.
Table 3. Enrichment analysis of network clusters identified by the edge betweenness algorithm.
| Cluster | Size | Core_Member | Top_Set | Top_OddsRatio | Top_PValue | Top_FDR |
|---|---|---|---|---|---|---|
| Cluster_1 | 40 | PPARA | 160977 | 68.83 | 0 | 0.00e+00 |
| Cluster_2 | 32 | HSP90AA1 | 1127556 | 855.48 | 0 | 0.00e+00 |
| Cluster_3 | 71 | RPS5; RPL19; POLR1B; RPS23; RPL15; RPL4; RPLP0; RPS7; RPL12; RPL10A | 491332 | 61.94 | 0 | 0.00e+00 |
| Cluster_4 | 70 | TP53 | 493498 | 10.79 | 0 | 2.89e-05 |
| Cluster_5 | 98 | FYN | 106034 | 23.18 | 0 | 0.00e+00 |
| Cluster_6 | 69 | POLR2A | 486891 | 37.15 | 0 | 0.00e+00 |
## R version 3.3.3 (2017-03-06)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X Yosemite 10.10.5
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] DEGandMore_0.0.0.9000 snow_0.4-2 igraph_1.1.2
## [4] awsomics_0.0.0.9000 GenomicRanges_1.26.4 GenomeInfoDb_1.10.3
## [7] IRanges_2.8.2 S4Vectors_0.12.2 BiocGenerics_0.20.0
## [10] htmlwidgets_0.9 DT_0.2 yaml_2.1.16
## [13] knitr_1.18 rmarkdown_1.9.8 RoCA_0.0.0.9000
## [16] RCurl_1.95-4.9 bitops_1.0-6 devtools_1.13.4
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.14 XVector_0.14.1 magrittr_1.5 zlibbioc_1.20.0
## [5] highr_0.6 stringr_1.2.0 tools_3.3.3 withr_2.1.1
## [9] htmltools_0.3.6 rprojroot_1.3-2 digest_0.6.13 memoise_1.1.0
## [13] evaluate_0.10.1 stringi_1.1.6 backports_1.1.2 jsonlite_1.5
## [17] pkgconfig_2.0.1
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